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Identification of overlay differentially expressed genes in both rats and goats with blast lung injury through comparative transcriptomics

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Chinese Journal of Traumatology 2024年第1期27卷 34-41页

作者： Hong Wang Jun-Hong Gao Xiao-Lin Fan Qing Lu Liang Li Ning Ma Qi Wang Yu-Hao Zhang Xi'an Key Laboratory of Toxicology and biological Effects Research Center for Toxicological and Biological EffectsInstitute for Hygiene of Ordnance IndustryXi'an710065China

Purpose:To identify the potential target genes of blast lung injury(BLI)for the diagnosis and treatment.Methods:This is an experimental study.The BLI models in rats and goats were established by conducting a fuel-air explosive power test in an unobstructed environment,which was subsequently validated through hematoxylin-eosin staining.Transcriptome sequencing was performed on lung tissues from both goats and rats.Differentially expressed genes were identified using the criteria ofq≤0.05 and|log2 fold change|≥1.Following that,enrichment analyses were conducted for gene ontology and the Kyoto Encyclopedia of Genes and Genomes pathways.The potential target genes were further confirmed through quantitative real-time polymerase chain reaction and enzyme linked immunosorbent assay.Results:Observations through microscopy unveiled the presence of reddish edema fluid,erythrocytes,and instances of focal or patchy bleeding within the alveolar cavity.Transcriptome sequencing analysis identified a total of 83 differentially expressed genes in both rats and goats.Notably,49 genes exhibited a consistent expression pattern,with 38 genes displaying up-regulation and 11 genes demonstrating down-regulation.Enrichment analysis highlighted the potential involvement of the interleukin-17 signaling pathway and vascular smooth muscle contraction pathway in the underlying mechanism of BLI.Furthermore,the experimental findings in both goats and rats demonstrated a strong association between BLI and several key genes,including anterior gradient 2,ankyrin repeat domain 65,bactericidal/permeability-increasing fold containing family A member 1,bactericidal/permeability-increasing fold containing family B member 1,and keratin 4,which exhibited up-regulation.Conclusions:Anterior gradient 2,ankyrin repeat domain 65,bactericidal/permeability-increasing fold containing family A member 1,bactericidal/permeability-increasing fold containing family B member 1,and keratin 4 hold potential as target genes for the prognosis,diagnosis,and treatment of BL

关键词： Blast lung injury Transcriptomic Target genes Differentially expressed genes

Induced pluripotent stem cells(iPSCs):molecular mechanisms of induction and applications

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Signal Transduction and Targeted Therapy 2024年第5期9卷 2065-2090页

作者： Jonas Cerneckis Hongxia Cai Yanhong Shi Department of Neurodegenerative Diseases Beckman Research Institute of City of HopeDuarteCA 91010USA Irell&Manella Graduate School of biological Sciences Beckman Research Institute of City of HopeDuarteCA 91010USA

The induced pluripotent stem cell(iPSC)technology has transformed in vitro research and holds great promise to advance regenerative medicine.iPSCs have the capacity for an almost unlimited expansion,are amenable to genetic engineering,and can be differentiated into most somatic cell types.iPSCs have been widely applied to model human development and diseases,perform drug screening,and develop cell therapies.In this review,we outline key developments in the iPSC field and highlight the immense versatility of the iPSC technology for in vitro modeling and therapeutic applications.We begin by discussing the pivotal discoveries that revealed the potential of a somatic cell nucleus for reprogramming and led to successful generation of iPSCs.We consider the molecular mechanisms and dynamics of somatic cell reprogramming as well as the numerous methods available to induce pluripotency.Subsequently,we discuss various iPSC-based cellular models,from mono-cultures of a single cell type to complex three-dimensional organoids,and how these models can be applied to elucidate the mechanisms of human development and diseases.We use examples of neurological disorders,coronavirus disease 2019(COVID-19),and cancer to highlight the diversity of disease-specific phenotypes that can be modeled using iPSC-derived cells.We also consider how iPSC-derived cellular models can be used in high-throughput drug screening and drug toxicity studies.Finally,we discuss the process of developing autologous and allogeneic iPSC-based cell therapies and their potential to alleviate human diseases.

关键词： mechanisms programming holds

How variable progenitor clones construct a largely invariant neocortex

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National Science Review 2024年第1期11卷 129-144页

作者： Zhongfu Shen Jiajun Yang Qiangqiang Zhang Kuiyu Wang Xiaohui Lv Xiaolin Hu Jian Ma Song-Hai Shi New Cornerstone Science Laboratory IDG/McG overn Institute for Brain Research Tsinghua-Peking Center for Life Sciences Beijing Frontier Research Center for Biological Structure School of Life Sciences Tsinghua University Department of Computer Sciences Tsinghua University College of Life Sciences Nankai University Chinese institute for Brain research

The neocortex contains a vast collection of diverse neurons organized into distinct layers. While nearly all neocortical neurons are generated by radial glial progenitors(RGPs), it remains largely unclear how a complex yet organized neocortex is constructed reliably and robustly. Here, we show that the division behavior and neuronal output of RGPs are highly constrained with patterned variabilities to support the reliable and robust construction of the mouse neocortex. The neurogenic process of RGPs can be well-approximated by a consistent Poisson-like process unfolding over time, producing deep to superficial layer neurons progressively. The exact neuronal outputs regarding layer occupation are variable; yet, this variability is constrained systematically to support all layer formation, largely reflecting the variable intermediate progenitor generation and RGP neurogenic entry and exit timing differences. Together, these results define the fundamental features of neocortical neurogenesis with a balanced reliability and variability for the construction of the complex neocortex.

关键词： neocortex radial glial progenitor intermediate progenitor neurogenesis clonal variability layer formation

Lactiplantibacillus plantarum FRT4 attenuates high-energy low-protein dietinduced fatty liver hemorrhage syndrome in laying hens through regulating gut-liver axis

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Journal of Animal Science and Biotechnology 2024年第3期15卷 1292-1311页

作者： Daojie Li Hongying Cai Guohua Liu Yunsheng Han Kai Qiu Weiwei Liu Kun Meng Peilong Yang Key Laboratory of Feed Biotechnology of Ministry of Agriculture and Rural Affairs Institute of Feed ResearchChinese Academy of Agricultural SciencesBeijing 100081China National Engineering research Center of biological Feed Beijing 100081China

Background Fatty liver hemorrhage syndrome(FLHS)becomes one of the most major factors resulting in the laying hen death for caged egg production.This study aimed to investigate the therapeutic effects of Lactiplantibacillus plan-tarum(Lp.plantarum)FRT4 on FLHS model in laying hen with a focus on liver lipid metabolism,and gut microbiota.Results The FLHS model of laying hens was established by feeding a high-energy low-protein(HELP)diet,and the treatment groups were fed a HELP diet supplemented with differential proportions of Lp.plantarum FRT4.The results indicated that Lp.plantarum FRT4 increased laying rate,and reduced the liver lipid accumulation by regulating lipid metabolism(lipid synthesis and transport)and improving the gut microbiota composition.Moreover,Lp.plan-tarum FRT4 regulated the liver glycerophospholipid metabolism.Meanwhile,“gut-liver”axis analysis showed that there was a correlation between gut microbiota and lipid metabolites.Conclusions The results indicated that Lp.plantarum FRT4 improved the laying performance and alleviated FLHS in HELP diet-induced laying hens through regulating“gut-liver”axis.Our findings reveal that glycerophospholipid metabolism could be the underlying mechanism for the anti-FLHS effect of Lp.plantarum FRT4 and for future use of Lp.plantarum FRT4 as an excellent additive for the prevention and mitigation of FLHS in laying hens.

关键词： Fatty liver hemorrhage syndrome Gut microbiota Lactiplantibacillus plantarum FRT4 Laying hens Lipid metabolism

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Integrated neural tracing and in-situ barcoded sequencing reveals the logic of SCN efferent circuits in regulating circadian behaviors

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Science China(Life Sciences) 2024年第3期67卷 518-528页

作者： Meimei Liao Xinwei Gao Chen Chen Qi Li Qingchun Guo He Huang Erquan Zhang Dapeng Ju College of biological Sciences China Agriculture UniversityBeijing 100193China National institute of biological Sciences(NIBS) Beijing 102206China Chinese institute for Brain research Beijing 102206China School of Biomedical Engineering Capital Medical UniversityBeijing 100069China Department of Anesthesiology The Second Affiliated HospitalChongqing Medical UniversityChongqing 401336China Tsinghua institute of Multidisciplinary Biomedical research Tsinghua UniversityBeijing 102206China

The circadian clock coordinates rhythms in numerous physiological processes to maintain organismal homeostasis. Since the suprachiasmatic nucleus(SCN) is widely accepted as the circadian pacemaker, it is critical to understand the neural mechanisms by which rhythmic information is transferred from the SCN to peripheral clocks. Here, we present the first comprehensive map of SCN efferent connections and suggest a molecular logic underlying these projections. The SCN projects broadly to most major regions of the brain, rather than solely to the hypothalamus and thalamus. The efferent projections from different subtypes of SCN neurons vary in distance and intensity, and blocking synaptic transmission of these circuits affects circadian rhythms in locomotion and feeding to different extents. We also developed a barcoding system to integrate retrograde tracing with in-situ sequencing, allowing us to link circuit anatomy and spatial patterns of gene expression. Analyses using this system revealed that brain regions functioning downstream of the SCN receive input from multiple neuropeptidergic cell types within the SCN, and that individual SCN neurons generally project to a single downstream brain region.This map of SCN efferent connections provides a critical foundation for future investigations into the neural circuits underlying SCNmediated rhythms in physiology. Further, our new barcoded tracing method provides a tool for revealing the molecular logic of neuronal circuits within heterogeneous brain regions.

关键词： circadian rhythms SCN output circuit neural tracing barcoded GFP in situ sequencing

Knockout of miR396 genes increases seed size and yield in soybean

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Journal of Integrative Plant Biology 2024年第6期66卷 1148-1157页

作者： Hongtao Xie Fei Su Qingfeng Niu Leping Geng Xuesong Cao Minglei Song Jinsong Dong Zai Zheng Rui Guo Yang Zhang Yuanwei Deng Zhanbo Ji Kang Pang Jian-Kang Zhu Jianhua Zhu School of Life Sciences Anhui Agricultural University research Center for biological Breeding Technology Research Institute of Frontier Science Anhui Agricultural University Bellagen Biotechnology Co.Ltd institute of Crop Sciences/National Nanfan research institute Chinese Academy of Agricultural Sciences Key Laboratory of Gene Editing Technologies (Hainan) Ministry of Agriculture and Rural Affairs Southern University of Science and Technology Hainan Yazhou Bay Seed Laboratory

Yield improvement has long been an important task for soybean breeding in the world in order to meet the increasing demand for food and animal feed. mi R396 genes have been shown to negatively regulate grain size in rice,but whether mi R396 family members may function in a similar manner in soybean is unknown. Here, we generated eight soybean mutants harboring different combinations of homozygous mutations in the six soybean mi R396genes through genome editing with clustered regularly interspaced palindromic repeats(CRISPR)/CRISPR-associated nuclease(Cas)12SF01 in the elite soybean cultivar Zhonghuang 302(ZH302). Four triple mutants (mir396aci, mir396acd, mir396adf, and mir396cdf), two quadruple mutants(mir396-abcd and mir396acfi), and two quintuple mutants(mir396abcdf and mir396bcdfi) were characterized. We found that plants of all the mir396 mutants produced larger seeds compared to ZH302 plants. Field tests showed that mir396adf and mir396cdf plants have significantly increased yield in growth zones with relatively high latitude which are suited for ZH302 and moderately increased yield in lower latitude. In contrast, mir396abcdf and mir396bcdfiplants have increased plant height and decreased yield in growth zones with relatively high latitude due to lodging issues, but they are suited for low latitude growth zones with increased yield without lodging problems.Taken together, our study demonstrated that loss-of-function of mi R396 genes leads to significantly enlarged seed size and increased yield in soybean, providing valuable germplasms for breeding high-yield soybean.

关键词： Cas12SF01 CRISPR/Cas miR396 seed size soybean yield

One-step construction of strongly coupled Co_(3)V_(2)O_(8)/Co_(3)O_(4)/MXene heterostructure via in-situ Co-F bonds for high performance all-solid-state asymmetric supercapacitors

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Rare Metals 2024年第2期43卷 682-691页

作者： Ji Zhou Bin-Bin Liu Hu Zheng Wen-Qing Ma Qian Li Cai-Xia Xu institute for Advanced Interdisciplinary research(iAIR) Collaborative Innovation Center of Technology and Equipment for Biological Diagnosis and Therapy in Universities of ShandongSchool of Chemistry and Chemical EngineeringUniversity of JinanJinan250022China

Co_(3)V_(2)O_(8)/Co_(3)O_(4)/Ti_(3)C_(2)T_(x) composite was easily synthesized via one-step succinct-operated hydrothermal process.The interconnected Co_(3)V_(2)O_(8)/Co_(3)O_(4) nanowires network can in-situ grow and anchor on the surface of Ti_(3)C_(2)T_(x) via the strong Co-F bonds and contribute tremendously to depress Ti_(3)C_(2)T_(x) self-restacking.Profiting from the synergistically interplayed effect among the multiple interfaces and high conductivity of Ti_(3)C_(2)T_(x) as well as outstanding stability of the as-designed nanostructure,the optimum Co_(3)V_(2)O_(8)/Co_(3)O_(4)/Ti_(3)C_(2)T_(x)electrode reaches a commendable specific capacitance(up to 3800 mF·cm^(−2)),great rate capability(80%capacitance retention after 20-times current increasing),and preeminent cycling stability(95.4%/85.5%retention at 7000th/20,000th cycle).Moreover,the all-solid-state asymmetric supercapacitor based on Co_(3)V_(2)O_(8)/Co_(3)O_(4)/Ti_(3)C_(2)T_(x) and active carbon can deliver a high energy density of 84.0μWh·cm^(−2) at the power energy of 3.2 mW·cm^(−2),and excellent cycling durability with 87.0%of initial capacitance retention upon 20,000 loops.This work provides a practicable pathway to tailor MXene-based composites for high-performance supercapacitor.

关键词： Ti_(3)C_(2)T_(x) Co_(3)V_(2)O_(8)/Co_(3)O_(4) Heterostructure Cathode Supercapacitor

New insights into nitric oxide biosynthesis underpin lateral root development

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Molecular Plant 2024年第5期17卷 691-693页

作者： Kapuganti Jagadis Gupta Nidhi Yadav Aprajita Kumari Gary J.Loake National institute for Plant Genome research Aruna Asaf Ali MargNew Delhi 110070India institute of Molecular Plant Sciences School of Biological SciencesUniversity of EdinburghEH93BF EdinburghUK Centre for Engineering Biology School of Biological SciencesUniversity of EdinburghEH93BF EdinburghUK

In recent years,nitric oxide(NO)has emerged as a key redox signaling molecule in plants functioning in the regulation of key developmental programs and the orchestration of responses to a plethora of environmental cues(Kolbert et al.,2019).The predominant route for the transfer of NO bioactivity is through S-nitrosylation,the addition of an NO moiety to a protein cysteine thiol to form an S-nitrosothiol(Yun et al.,2011).Specificity for this process is established by the structural constraints imposed by tertiary protein structure in gating access to given cysteine redox switches and associated proteins that can either facilitate the addition or removal of the NO moiety at these residues(Umbreen et al.,2018).

关键词： moiety addition redox

How do neurons age?A focused review on the aging of the microtubular cytoskeleton

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Neural Regeneration research 2024年第9期19卷 1899-1907页

作者： Brad Richardson Thomas Goedert Shmma Quraishe Katrin Deinhardt Amritpal Mudher School of biological Sciences University of SouthamptonSouthamptonUK institute of Developmental and Regenerative Medicine University of OxfordOxfordUK

Aging is the leading risk factor for Alzheimer’s disease and other neurodegenerative diseases. We now understand that a breakdown in the neuronal cytoskeleton, mainly underpinned by protein modifications leading to the destabilization of microtubules, is central to the pathogenesis of Alzheimer’s disease. This is accompanied by morphological defects across the somatodendritic compartment, axon, and synapse. However, knowledge of what occurs to the microtubule cytoskeleton and morphology of the neuron during physiological aging is comparatively poor. Several recent studies have suggested that there is an age-related increase in the phosphorylation of the key microtubule stabilizing protein tau, a modification, which is known to destabilize the cytoskeleton in Alzheimer’s disease. This indicates that the cytoskeleton and potentially other neuronal structures reliant on the cytoskeleton become functionally compromised during normal physiological aging. The current literature shows age-related reductions in synaptic spine density and shifts in synaptic spine conformation which might explain age-related synaptic functional deficits. However, knowledge of what occurs to the microtubular and actin cytoskeleton, with increasing age is extremely limited. When considering the somatodendritic compartment, a regression in dendrites and loss of dendritic length and volume is reported whilst a reduction in soma volume/size is often seen. However, research into cytoskeletal change is limited to a handful of studies demonstrating reductions in and mislocalizations of microtubule-associated proteins with just one study directly exploring the integrity of the microtubules. In the axon, an increase in axonal diameter and age-related appearance of swellings is reported but like the dendrites, just one study investigates the microtubules directly with others reporting loss or mislocalization of microtubule-associated proteins. Though these are the general trends reported, there are clear disparities between model organisms and brain

关键词： age-related changes aging cytoskeleton microtubules neuronal morphology